<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Dear all<div><br></div><div>I am trying to run the following command for using VEP. I am running local version of the ensembl database (v65). I am using perl version 5.14.2.</div><div><br></div><div><div>perl5.14.2 variant_effect_predictor.pl --output_file outfile.vep --species homo_sapiens --host host --user user --password password --port 1111 --db_version 65 --format vcf --buffer 1000000000 --terms ensembl --canonical --hgnc --cache --regulatory --protein --gene --condel b --polyphen b --sift b --force_overwrite --input_file infile.vcf -skip_db_check</div></div><div><br></div><div>I have VCF files generated for all chromosomes separately for 15 samples. The script works all good for all chromosomes for all samples except for chr14 and chr15.</div><div><br></div><div>Here is the log report after trying to run the script for chr14 and chr15.</div><div><br></div><div><div>Use of qw(...) as parentheses is deprecated at variant_effect_predictor.pl line 848.</div><div>2012-01-27 10:41:59 - Read existing cache info</div><div>2012-01-27 10:41:59 - Reading cached adaptor data</div><div>Use of uninitialized value $_[3] in join or string at ensembl-api/ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 3497.</div><div>2012-01-27 10:41:59 - INFO: Defined host ##### is different from cached </div><div>2012-01-27 10:41:59 - Starting...</div><div>2012-01-27 10:42:03 - Read 131269 variants into buffer</div><div>2012-01-27 10:42:04 - Analyzing chromosome 14</div><div>2012-01-27 10:42:04 - Reading transcript data from cache and/or database</div><div>[> ] [ 0% ]</div><div>Can't call method "fetch_by_region" on unblessed reference at ensembl-api/ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 2144, <GEN0> line 131296.</div></div><div><br></div><div>I have tried downloading the cache again and see if that helps. However, I am not able to run it on these two chromosomes at all. Could you please let me know how to correct this issue?</div><div><br></div><div>I have attached two vcf files as examples to test the code on your end.</div><div><br></div><div>NB: it is the chromosome 14 and 15 that are the issue. rest are all fine and giving appropriate results.</div><div><br></div><div><br></div><div>Any help is greatly appreciated.</div><div><br></div><div>Kind regards</div></body></html>